MSA 4.05 – Microsatellite Analyzer

MSA 4.05

:: DESCRIPTION

The MSA software tool was designed to handle large microsatellite data sets. To avoid error prone reformatting, MSA uses a simple input format, very close to a simple spreadsheet.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

MSA

:: MORE INFORMATION

Citation:

Dieringer, Daniel & Schlötterer, Christian (2003)
Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets.
Molecular Ecology Notes 3 (1), 167-169

PDA 1.0.3 – Phylogenetic Diversity Analyzer

PDA 1.0.3

:: DESCRIPTION

PDA (Phylogenetic Diversity Algorithm) is a software tool to analyze various aspects of PD and PD-related measures based on both phylogenetic trees and networks

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

PDA

:: MORE INFORMATION

Citation:

Split diversity in constrained conservation prioritization using integer linear programming.
Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A.
Methods Ecol Evol. 2015 Jan;6(1):83-91.

seqsee 1.6 – Protein Sequence Analyzer

seqsee 1.6

:: DESCRIPTION

SEQSEE (SEQuence SEEr) is a multi-purpose menu-driven suite of programs designed to provide a fully integrated analysis of protein sequences and protein databases. It contains rapid database searching, flexible pattern matching and multiple sequence alignment as well as a large number of structural analysis and prediction programs.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

seqsee

:: MORE INFORMATION

Citation

David S. Wishart, Robert F. Boyko, Leigh Willard, Frederic M. Richards and Brian D. Sykes
SEQSEE: a comprehensive program suite for protein sequence analysis
Comput Appl Biosci (1994) 10 (2): 121-132.

TMM@ – Trans-Membrane alpha-helical Movement Analyzer

TMM@

:: DESCRIPTION

TMM@ (TransMembrane α-helical Mobility analyzer) is a web-application uses NMA to characterize the propensity of transmembrane α-helices to be displaced. Starting from a structure file at the PDB format, the server computes the normal modes of the protein and identifies which helices in the bundle are the most mobile. Each analysis is performed independently from the others and results can be visualized using only a web browser.

::DEVELOPER

Lars Skjærven and Nathalie Reuter , Uni Computing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

TMM@: a web application for the analysis of transmembrane helix mobility
Lars Skjaerven, Inge Jonassen and Nathalie Reuter
BMC Bioinformatics 2007, 8:232

JANE – EST Analyzer

JANE

:: DESCRIPTION

JANE (Just Analyze Nucleotides and ESTs) provides a feasible plan for rapid analysis of EST sequences using a related genome as template to align all the ESTs. The homology modeling results in a virtual genome, with annotation for systematical analysis.

::DEVELOPER

JANE Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Nov 29;10:391.
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
Liang C, Schmid A, López-Sánchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T.

GPS-MBA 1.0 – MHC-binding Analyzer

GPS-MBA 1.0

:: DESCRIPTION

GPS-MBA (MHC Binding Analyzer) software package was developed for the prediction of I-Ag7 and HLA-DQ8 epitopes. Using experimentally identified epitopes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted and improved.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

WIndows / Linux / MacOsX
Java

:: DOWNLOAD

GPS-MBA

:: MORE INFORMATION

Citation

GPS-MBA: Computational analysis of MHC Class II Epitopes in Type 1 Diabetes
Ruikun Cai, Zexian Liu, Jian Ren, Chuang Ma, Tianshun Gao, Yanhong Zhou, Qing Yang and Yu Xue.
PLoS ONE, 2012, 7(3): e33884.

PDA 2.0 – Pooled DNA Analyzer

PDA 2.0

:: DESCRIPTION

PDA, Pipeline Diversity Analysis, is a collection of programs and modules, mainly written in Perl, that automatically can:

explore for potentially polymorphic sequences from a large source of heterogeneous DNA,
extract and sort them out by gene, species and extent of similarity,
align the different groups, and
estimate the genetic diversity in different functional regions.

::DEVELOPER

Sònia Casillas and Antonio Barbadilla. Genomics, Bioinformatics and Evolution Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
Perl

:: DOWNLOAD

PDA

:: MORE INFORMATION

Citation

Sònia Casillas and Antonio Barbadilla (2006).
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA.
Nucleic Acids Res. 34 (Web Server issue): W632-W634; doi: 10.1093/nar/gkl080

SVA 1.10 – Sequence Variant Analyzer

SVA 1.10

:: DESCRIPTION

SVA is a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits.

::DEVELOPER

Dongliang Ge, PhD.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

SVA

:: MORE INFORMATION

Citation

Ge,Ruzzo, Shianna,He,Pelak, Heinzen, Need, Cirulli, Maia, Dickson, Zhu,Singh, Allen, Goldstein (2011),
“SVA: software for annotating and visualizing sequenced human genomes“,
Bioinformatics, 27:1998-2000

MPDA 20081110 – Microarray Pooled DNA Analyzer

MPDA 20081110

:: DESCRIPTION

MPDA (Microarray Pooled DNA Analyzer) is an innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.

::DEVELOPER

Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

::REQUIREMENTS

Linux/Windows/MacOsX
MATLAB®

:: DOWNLOAD

MPDA

:: MORE INFORMATION

Citation

Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L. T. Yu, Mitchell B. Diccianni, Jer-Yuan Wu, Yuarn-Tsong Chen, Cathy S. J. Fann (2008).
MPDA: Microarray Pooled DNA Analyzer.
BMC Bioinformatics. 9:196.

NSA 3.3 – Nucleotide Sequence Analyzer

NSA 3.3

:: DESCRIPTION

NSA (Nucleotide Sequence Analyzer) may be used to handled nucleotidic sequences in order to compute a number of characteristics (such as haplotypes, composition, sites, haplogroups, distances, …..) and to create a variety of export files usable with other available softwares.

::DEVELOPER

Daniel Montagnon PhD

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

NSA

:: MORE INFORMATION

If you download and use this software please register to be informed for new release and modifications.